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In the first act Lieutenant B.F. Pinkerton, a sailor with the USS Abraham Lincoln in the port of Nagasaki marries Cio-Cio-San , or "Butterfly," a 15-year-old Japanese geisha. The Matchmaker Goro has arranged the wedding contract and rented a little hillside house for the newlyweds. The American consul Sharpless, a kind man, begs Pinkerton to forego this plan, when he learns that Butterfly innocently believes the marriage to be binding. (In fact, Pinkerton may revoke the contract whenever he tires of the "marriage.") The lieutenant laughs at Sharpless’s concern, and the bride appears with her geisha friends, joyous and smiling. Sharpless learns that, to show her trust in Pinkerton, she has renounced the faith of her ancestors and so she can never return to her own people. (Butterfly: "Hear what I would tell you.") Pinkerton also learns that she is the daughter of a disgraced samurai who committed seppuku, and so the little girl was sold to be trained as a geisha. The marriage contract is signed and the guests are drinking a toast to the young couple when the bonze, a Buddhist monk, (uncle of Cio-Cio-San, and presumably having entered the monastery in disgrace after the father’s seppuku) enters, uttering imprecations against her for having taken to the foreign faith, and induces her friends and relatives to abandon her. Pinkerton, annoyed, hurries the guests off, and they depart in anger. With loving words he consoles the weeping bride, and the two begin their new life happily. (Duet, Pinkerton, Butterfly: "Just like a little squirrel"; Butterfly: "But now, beloved, you are the world"; "Ah! Night of rapture.")

Act II

Pinkerton’s tour of duty is over, and he has returned to the United States, after promising Butterfly to return "When the robins nest again." Three years have passed. Butterfly’s faithful servant Suzuki rightly suspects that he has abandoned them, but is upbraided for want of faith by her trusting mistress. (Butterfly: "Weeping? and why?") Meanwhile, Sharpless has been sent by Pinkerton with a letter telling Butterfly that he has married an American wife. Butterfly (who cannot read English) is enraptured by the sight of her lover’s letter and cannot conceive that it contains anything but an expression of his love. Seeing Butterfly’s joy, Sharpless cannot bear to hurt her with the truth. When Goro brings Yamadori, a rich suitor, to meet Butterfly, she refuses to consider his suit, telling them with great offense that she is already married. Goro explains that a wife abandoned is a wife divorced, but Butterfly declares defiantly, "That may be Japanese custom, but I am now an American." Sharpless cannot move her, and at last, as if to settle all doubt, Butterfly proudly presents her fair-haired child. "Can my husband forget this?" she challenges. Butterfly explains that the boy’s name is "Sorrow," but when when his father returns, his name will be "Joy." The consul departs sadly. But Butterfly has long been a subject of gossip, and Suzuki catches the duplicitous Goro spreading more. Just as things cannot seem worse, distant guns salute the new arrival of a man-of-war, the Abraham Lincoln, Pinkerton’s ship. Butterfly and Suzuki, in great excitement, deck the house with flowers, and array themselves and the child in gala dress. All three peer through shoji doors to watch for Pinkerton’s coming. As night falls, a long orchestral passage with choral humming (the "humming chorus") plays. Suzuki and the child gradually fall asleep - but Butterfly, alert and sleepless, never stirs.

Act III

Act three opens at dawn with Butterfly still intently watching. Suzuki awakens and brings the baby to her. (Butterfly: "Sweet, thou art sleeping.") Suzuki persuades the exhausted Butterfly to rest. Pinkerton and Sharpless arrive and tell Suzuki the terrible truth: Pinkerton has abandoned Butterfly for an American wife. The lieutenant is stricken with guilt and shame (Pinkerton: "Oh, the bitter fragrance of these flowers!"), but is too much of a coward to tell Butterfly himself. He has assigned this awful task to his wife, Kate. Suzuki, at first violently angry, is finally persuaded to listen as Sharpless assures her that Mrs. Pinkerton will care for the child if Butterfly will give him up. Pinkerton departs. Suzuki brings Butterfly into the room. She is radiant, expecting to find her husband, but is confronted instead by Pinkerton’s new wife. As Sharpless watches silently, Kate begs Butterfly’s forgiveness and promises to care for her child if she will surrender him to Pinkerton. Butterfly receives the truth with apathetic calmness, politely congratulates her replacement, and asks Kate to tell her husband that in half an hour he may have the child. She herself will "find peace." She bows her visitors out, and is left alone with young Sorrow. She bids a pathetic farewell to her child (Finale, Butterfly: "You, O beloved idol!"), blindfolds him, and puts a doll and small American flag in his hands. She takes her father’s sword--the weapon with which he made his suicide--and reads its inscription: "To die with honour, when one can no longer live with honour." She takes the sword and a white scarf behind a screen, and emerges a moment later with the scarf wrapped round her throat. She embraces her child for the last time and sinks to the floor. Pinkerton and Sharpless rush in and discover the dying girl. The lieutant cries out Butterfly’s name in anguish as the curtain falls.